We used the publicly available JHU Biobank RNASeq data stored in project : syn20812185 for this analysis.
We then used TMM normalization to prepare the dataset for differential gene expression analysis.
We used limma-edgeR based analysis to find differentially expressed genes in the TMM normalized dataset.
A point to note:
The plot below shows genes that are significantly overexpressed in MPNST compared to PNF or NF (logFC > 4) in red. The dots in blue refer to genes that are significantly underexpressed in MPNST compared to PNF or NF (logFC < -4). The thresholds of fold change have been arbitrarily chosen for ease of visualization in the volcano plot shown below.
Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
## [1] "Enrichment Plot of Cluster 1 genes"
## [1] "Enrichment Plot of Cluster 2 genes"
## [1] "Enrichment Plot of Cluster 3 genes"
## [1] "List of genes in Cluster 3"
## [1] "AMPH" "ARHGAP11A" "BIRC5" "BYSL" "CACNA1A" "CCNA2"
## [7] "CCNB1" "CCNF" "CDC20" "CDCA5" "CILP2" "COL13A1"
## [13] "CYTL1" "ELFN1" "EPOP" "FAM155A" "FANCI" "GALNT14"
## [19] "HAPLN3" "IGF2BP3" "KRT18" "NCAPG" "NCAPH" "NUSAP1"
## [25] "OSBPL6" "PLK1" "PMAIP1" "PRC1" "PTTG1" "RAB42"
## [31] "RRM2" "SEC61G" "SERINC2" "SIX4" "SLC16A3" "SLC39A11"
## [37] "SPAG5" "TNFSF9" "TPX2" "TSTA3" "ULBP1"
Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue
## [1] "Enrichment Plot of Cluster 1 genes"
## [1] "Enrichment Plot of Cluster 2 genes"
## [1] "List of genes in Cluster 2 (cluster with PLK1)"
## [1] "ACAN" "ADAMTS17" "APBA2" "BIRC5" "CACNA1A" "CBX2"
## [7] "CCNA2" "CCNF" "CDC20" "CDCA5" "CILP2" "COL13A1"
## [13] "DPYSL4" "ELFN1" "EPOP" "GALNT14" "HOXA5" "IGF2BP3"
## [19] "IL4I1" "JPH4" "KIF15" "KIFC1" "KRT8" "LRRN2"
## [25] "MSX2" "NCAPG" "NRK" "PLK1" "RAB42" "SAMD14"
## [31] "SERINC2" "SHISA2" "SIX1" "SIX4" "SNCAIP" "SPEG"
## [37] "SUGCT" "TK1" "TNFSF9" "TRIM59" "ULBP1" "VPS37D"
## [1] "Enrichment Plot of Cluster 3 genes"
## [1] "Enrichment Plot of Cluster 4 genes"